This study aimed to assess the phylogenetic relationship of Vietnamese mouse deer from the Southern ofVietnam using cytochrome b. Eleven mouse deer samples (CT1 to CT9, and LD1- LD2)from Lam Dong Province and Cat Tien National Park of DongNaiProvince were used for this investigation. The sequence analysis revealed 37 polymorphic sites,in which 13 variable positions (14328, 14337, 14400, 14427, 14436, 14466, 14523, 14526, 14530, 14537, 14541, 14544, 14550) were observed in Vietnamese mouse deer.Moreover,Vietnamese mouse deer showed the lowest genetic distance withTragulusjavanicus (0.031 ± 0.014)compared toTragulusnapu (0.051 ± 0.022)andTraguluskanchil (0.035 ± 0.016). Phylogenetic tree building showed that Vietnamese mouse deer were clustered in distinct group with 100% bootstrap probability. In addition, the variable position at 14325 (A  G) contributed to the separation of CT2, CT4, CT7, and CT8 in one group with 64% bootstrap probability.